Contacts of the helix formed by residues 271 - 287 (chain A) in PDB entry 3UMO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ALA* 1.3 78.8 - - - +
272A LEU* 1.3 64.6 + - - +
273A GLU* 3.6 9.0 + - - +
274A GLU* 3.0 28.4 + - - +
275A MET* 3.0 21.5 + - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 4.7 7.2 - - + +
222A VAL* 4.9 0.9 - - + -
232A GLY* 3.6 28.3 - - - +
233A VAL 4.4 9.0 - - - +
234A ASP* 3.5 34.2 + - + +
237A ASN* 3.8 32.5 - - + +
239A ILE* 4.1 13.5 - - + -
270A ALA 3.9 0.2 + - - -
271A SER* 1.3 71.8 - - - +
273A GLU* 1.3 58.4 + - - +
275A MET* 3.3 30.9 + - + +
276A VAL* 2.9 41.7 + - + +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ILE* 3.5 32.7 - - + +
271A SER* 3.2 8.4 + - - +
272A LEU* 1.3 78.8 - - - +
274A GLU* 1.3 58.1 + - - +
276A VAL* 3.4 1.4 + - - +
277A ARG* 2.9 77.0 + - + +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 2.9 32.4 + - + +
268A GLU* 4.8 1.6 - - - +
270A ALA* 4.0 14.6 - - + +
271A SER* 3.0 22.5 + - - +
273A GLU* 1.3 78.4 - - - +
275A MET* 1.3 63.6 + - - +
277A ARG* 3.8 6.6 - - - +
278A PHE* 3.0 27.0 + - - +
304A TYR* 3.2 25.3 + - - +
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Residues in contact with MET 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.1 16.2 - - + -
220A ARG* 4.1 22.9 - - - -
222A VAL* 3.8 23.3 - - + -
262A MET* 3.3 42.9 - - + +
265A LYS* 3.8 17.2 - - + +
266A LEU* 4.4 12.1 - - - -
270A ALA* 5.1 3.1 - - + +
271A SER 3.0 17.2 + - - +
272A LEU* 3.5 32.5 - - + +
274A GLU* 1.3 77.6 - - - +
276A VAL* 1.3 60.2 + - + +
278A PHE* 3.5 1.9 + - - +
279A GLY 2.9 22.5 + - - -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A VAL* 4.0 18.6 - - + -
230A ALA* 4.1 28.0 - - + +
232A GLY* 3.9 22.2 - - - +
239A ILE* 3.6 17.9 - - + -
241A VAL* 3.7 24.5 - - + -
258A MET* 4.8 0.7 - - - +
262A MET* 4.4 5.8 - - - -
272A LEU* 2.9 25.0 + - + +
275A MET* 1.3 74.2 - - + +
277A ARG* 1.3 60.8 + - - +
279A GLY* 3.2 0.7 + - - -
280A VAL* 2.8 28.8 + - - +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLN 5.8 0.2 + - - -
241A VAL* 4.0 32.8 - - + +
273A GLU* 2.9 61.4 + - - +
274A GLU* 3.8 5.2 - - - +
276A VAL* 1.3 76.8 - - - +
278A PHE* 1.3 57.3 + - - +
280A VAL 3.4 0.2 + - - -
281A ALA* 2.9 25.1 + - - +
304A TYR* 3.8 13.2 - - + -
307A LEU* 3.0 48.8 + - + +
308A SER* 3.8 18.8 + - - +
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.0 20.0 - - + -
261A ALA* 3.3 46.5 - - + +
264A LEU* 4.7 10.5 - - + -
265A LYS* 3.7 31.0 - - + -
274A GLU 3.0 18.6 + - - +
275A MET 3.9 0.2 - - - +
277A ARG* 1.3 75.8 - - - +
279A GLY* 1.3 57.6 + - - +
281A ALA* 3.3 1.9 + - - +
282A ALA* 2.9 25.6 + - - +
297A HIS* 6.5 1.3 - + - -
300A THR* 3.7 25.6 - - + -
301A GLN* 5.5 2.0 - - - -
304A TYR* 3.7 29.3 - + + -
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A MET* 3.4 29.1 - - - +
261A ALA* 3.9 2.2 - - - -
262A MET* 3.6 25.5 - - - +
275A MET 2.9 10.9 + - - -
276A VAL 3.2 2.9 + - - -
278A PHE* 1.3 77.8 - - - +
280A VAL* 1.3 57.0 + - - +
282A ALA 3.4 0.5 + - - -
283A GLY 2.9 24.9 + - - -
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY 4.0 0.2 - - - -
230A ALA* 3.9 14.6 - - + +
241A VAL* 3.8 34.3 - - + +
243A PRO* 3.9 35.0 - - + -
258A MET* 3.5 15.7 - - + +
276A VAL 2.8 22.3 + - - +
277A ARG 3.8 3.1 - - - +
279A GLY* 1.3 71.0 - - - +
281A ALA* 1.3 58.9 + - - +
284A SER* 2.9 31.2 + - - +
303A ILE* 5.3 0.4 - - + -
307A LEU* 4.1 6.1 - - + -
313A ATP 3.5 15.0 - - - +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ARG 2.9 17.6 + - - +
278A PHE 3.6 5.2 - - - +
279A GLY 3.3 0.2 - - - -
280A VAL* 1.3 77.2 - - - +
282A ALA* 1.3 56.5 + - - +
285A ALA* 2.8 30.7 + - - +
300A THR* 3.5 27.3 - - + +
303A ILE* 3.6 19.2 - - + +
304A TYR* 3.5 24.0 - - + +
307A LEU* 4.1 0.4 - - + +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.2 2.0 - - + -
257A SER* 3.5 16.9 - - - +
261A ALA* 3.4 31.4 - - + -
278A PHE 2.9 7.1 + - - +
279A GLY 4.0 0.7 - - - +
281A ALA* 1.3 74.3 - - - +
283A GLY* 1.3 67.8 + - - +
285A ALA 3.3 0.2 + - - -
286A ALA 2.9 18.9 + - - -
295A CYS* 3.3 18.3 - - - +
300A THR* 3.6 21.7 - - + +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ALA* 3.4 21.8 - - - +
258A MET 4.0 1.9 - - - +
279A GLY 2.9 17.1 + - - -
280A VAL 3.8 0.9 - - - -
282A ALA* 1.3 76.5 - - - +
284A SER* 1.3 60.1 + - - +
286A ALA* 3.3 16.6 + - - +
287A THR* 3.4 11.6 - - - +
313A ATP 3.3 23.1 - - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PRO* 3.2 21.4 - - - +
244A PRO* 5.4 0.7 - - - -
280A VAL 2.9 15.5 + - - -
281A ALA* 5.0 0.2 - - - -
283A GLY* 1.3 73.3 - - - +
285A ALA* 1.3 64.5 + - - +
287A THR* 2.7 21.8 + - - -
288A LEU* 3.6 8.7 - - - +
303A ILE* 4.0 14.8 - - - -
313A ATP 3.0 43.5 + - - -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA 2.8 20.5 + - - +
282A ALA 3.6 3.1 - - - +
284A SER* 1.3 76.8 - - - +
286A ALA* 1.3 62.9 + - - +
288A LEU* 3.1 23.0 + - - +
289A ASN* 4.0 9.2 + - - -
295A CYS* 4.0 6.5 - - + -
299A ASP* 3.8 11.7 - - + +
300A THR* 3.3 35.7 - - - +
303A ILE* 3.6 8.2 - - + +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A SER 4.2 0.2 - - - -
252A VAL 4.5 1.6 - - - +
253A GLY 3.8 15.3 - - - +
254A ALA* 3.9 5.4 - - - +
257A SER* 3.5 25.6 - - - +
282A ALA 2.9 8.6 + - - +
283A GLY 3.3 11.7 - - - +
284A SER 3.2 0.2 - - - -
285A ALA* 1.3 77.8 - - - +
287A THR* 1.3 60.5 - - - +
288A LEU 3.2 1.0 + - - -
289A ASN* 3.3 7.8 + - - +
293A ARG 3.7 2.9 - - - +
294A LEU* 4.0 4.9 - - - -
295A CYS* 3.7 14.3 - - - +
314A K 2.9 21.3 - - - -
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Residues in contact with THR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL 5.6 0.7 + - - -
248A SER* 3.4 24.3 - - - -
249A GLN 2.7 31.8 + - - -
250A SER 3.1 17.1 + - - -
251A THR* 4.2 8.1 - - - -
254A ALA* 4.1 9.4 - - + -
283A GLY 3.4 16.6 - - - +
284A SER* 2.7 16.9 + - - +
286A ALA* 1.3 76.0 - - - +
288A LEU* 1.3 57.9 + - - +
289A ASN 3.3 0.4 - - - -
313A ATP 3.6 37.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il